Commit c98cd115 authored by Christian Tischer's avatar Christian Tischer

Update image-ethics-and-data-integrity.md

parent a0cd6918
......@@ -30,18 +30,20 @@
'/>
### Activity: Explore image saving can change image content
### Activity: Save an image
![image](/uploads/284ad5edadf96234037f895a86338a58/image.png)
- Open image: `calibrated_16bit__cells_eres_noisy.tif`
- Inspect its content and take notes of some pixel values and coordinates
- Save the image in whatever format (e.g. tiff, png, gif, jpeg, ...)
- Note down the value and coordinate of the pixel at [218, 332]
- Save the image in **jpg** format
- Reopen the image
- Compare the image content to your notes, did it change?
- Compare the pixel to your notes, did it change?
Repeat above workflow, but now adjust the image display before saving.
Repeat above activity
Repeat above workflow, but now save it in a different format (e.g. tif, png).
- testing different formats for saving
- adjusting the image display before saving
### Formative assessment
......@@ -51,7 +53,6 @@ How can I ensure that image content is preserved during saving (one answer)?
2. I test it by checking pixel values and coordinates before and after saving.
3. I ask my colleagues in the lab, and do what they do.
## Lookup tables
### Concepts
......@@ -77,9 +78,9 @@ How can I ensure that image content is preserved during saving (one answer)?
- Open image: `xy_calibrated_16bit__nuclear_protein_control.tif`
- This image shows a nuclear protein in control cells.
- Open image: `xy_calibrated_16bit__nuclear_protein_treated.tif`
- The cells in this 'treated' image have been subjected to a drug.
- Inspect the images!
- Did the drug affect the nuclear protein?
- The cells in this image have been subjected to a drug.
- Inspect the images:
- Did the drug affect the amount of the nuclear protein?
- Adjust the lookup-tables (LUTs) of both images to be the same
- Add the LUT calibration to both images
......@@ -87,17 +88,33 @@ How can I ensure that image content is preserved during saving (one answer)?
What helps to scientifically convey image intensity information (multiple answers)?
1. Use a grayscale LUT whenever possible.
2. Color the images in the color of the fluorophore.
1. Use grayscale LUT whenever possible.
3. Add a LUT calibration bar.
4. Use the same LUT for all images.
5. Always adjust the LUT to the image's full bit-depth.
6. Never change the LUT of images! Always keep it as in the raw data.
5. Adjust the LUT to the image's full bit-depth.
6. Never change the LUT of images! Always keep it as is.
## 4-D image display
## 3-D image display
### Concepts
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
3-D data -> visualisation [label=" multiple options"];
visualisation -> scientific_message [label=" affects"];
}
'/>
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
3-D visualisation -> sum projection;
3-D visualisation -> max projection;
3-D visualisation -> slice animation;
}
'/>
### Activity: ...
......
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